• YASS
• Similarity search in DNA sequences
• version 1.16

** LICENSE

YASS is distributed under the dual-licence of the CeCILL (version 2 or any later version), and the GPL (version 2 or any later version), so you can use, modify and redistribute the program under these licences with almost no restriction.

** COMMAND SYNTAX

• Usage : yass [options] { file.mfas | file1.mfas file2.mfas }

  -h       display this Help screen
  -d <int>    0 : Display alignment positions (kept for compatibility)
              1 : Display alignment positions + alignments + stats (default)
              2 : Display blast-like tabular output
              3 : Display light tabular output (better for post-processing)
              4 : Display BED file output
              5 : Display PSL file output
  -r <int>    0 : process forward (query) strand
              1 : process Reverse complement strand
              2 : process both forward and Reverse complement strands (default)
  -o <str> Output file
  -l       mask Lowercase regions (seed algorithm only)
  -s <int> Sort according to
              0 : alignment scores
              1 : entropy
              2 : mutual information (experimental)
              3 : both entropy and score
              4 : positions on the 1st file
              5 : positions on the 2nd file
              6 : alignment % id
              7 : 1st file sequence % id
              8 : 2nd file sequence % id
              10-18 : (0-8) + sort by "first fasta-chunk order"
              20-28 : (0-8) + sort by "second fasta-chunk order"
              30-38 : (0-8) + sort by "both first/second chunks order"
              40-48 : equivalent to (10-18) where "best score for fst fasta-chunk" replaces "..."
              50-58 : equivalent to (20-28) where "best score for snd fasta-chunk" replaces "..."
              60-68 : equivalent to (70-78), where "sort by best score of fst fasta-chunk" replaces "..."
              70-78 : BLAST-like behavior : "keep fst fasta-chunk order", then trigger all hits for all good snd fasta-chunks
              80-88 : equivalent to (30-38) where "best score for fst/snd fasta-chunk"" replaces "..."
  -v       display the current Version
  
  -M <int> select a scoring Matrix (default 3):
           [Match,Transversion,Transition],(Gopen,Gext)
            0 : [  1, -3, -2],( -8, -2)   1 : [  2, -3, -2],(-12, -4)
            2 : [  3, -3, -2],(-16, -4)   3 : [  5, -4, -3],(-16, -4)
            4 : [  5, -4, -2],(-16, -4)
  -C <int>[,<int>[,<int>[,<int>]]]
           reset match/mismatch/transistion/other Costs (penalties)
           you can also give the 16 values of matrix (ACGT order)
  -G <int>,<int> reset Gap opening/extension penalties
  -L <real>,<real> reset Lambda and K parameters of Gumbel law
  -X <int>  Xdrop threshold score (default 25)
  -E <int>  E-value threshold (default 10)
  -e <real> low complexity filter :
            minimal allowed Entropy of trinucleotide distribution
            ranging between 0 (no filter) and 6 (default 2.80)
  
  -O <int> memory limit of the number of ungapped alignments (default 1000000)
  -S <int> Select sequence from the first multi-fasta file (default 0)
             * use 0 to select the full first multi-fasta file
  -T <int> forbid aligning too close regions (e.g. Tandem repeats)
           valid for single sequence comparison only (default 16 bp)
  
  -p <str> seed Pattern(s)
             * use '#' for match
             * use '@' for match or transition
             * use '-' or '_' for joker
             * use ',' for seed separator (max: 32 seeds)
             - example with one seed :
                yass file.fas -p  "#@#--##--#-##@#"
             - example with two complementary seeds :
                yass file.fas -p "##-#-#@#-##@-##,##@#--@--##-#--###"
             (default  "###-#@-##@##,###--#-#--#-###")
  -c <int> seed hit Criterion : 1 or 2 seeds to consider a hit (default 2)
  
  -t <real> Trim out over-represented seeds codes
            ranging between 0.0 (no trim) and +inf (default 0.001)
  -a <int> statistical tolerance Alpha (%) (default 5%)
  -i <int> Indel rate (%)                  (default 8%)
  -m <int> Mutation rate (%)               (default 25%)
  
  -W <int>,<int> Window <min,max> range for post-processing and grouping
                 alignments (default <64,65536>)
  -w <real> Window size coefficient for post-processing and grouping
            alignments (default 16)
            NOTE : -w 0 disables post-processing

Scoring System :

-M : choose a preselected matrix and gap opening and extension penalty

the default “-M 3” gives fowoling scores :

      +5 for match reward,
      -4 for transversion penalty,
      -2 for transition penalty,
      and

      -16 for gap opening penalty.
      -4  for gap extention penalty.

but you can also choose the

-C (,(,(,))) : choose a scoring system

if you give 2 parameters : match reward, mismatch penalty 3 parameters : match reward, transversion penalty, transition penalty 4 parameters : match reward, transversion penalty, transition penalty, other penalty (non ACGTU letters)

-G , : choose a gap opening and extension penalty

for gap opening penalty, gap extention penalty.

-d : choose Display preferences

  -d 0  gives maximal positions of alignments
  -d 1  gives ... + statistical parameters and quick alignments
        (it means that those alignments are computed using seeds
         as anchors, which is not always the best solution, but
         the fastest one)
  -d 2 blast like tabular output
  -d 3 "position - size" tiny display

-s : choose Sorting

it is possible to sort according to score (-s 1), positions on
the first (-s 4) or the second file (-s 5), and also, for
multifasta files to sort according to the first file chunks (-s 10
"to" 15), the secongd file chunks (-s 20 "to" 25) or both of them
(-s 30 "to" 35)

-S : choose the first multifasta chunk

this parameter is by default 1, since it selects the first chunk
of the first multifasta file : you can choose any valid chunk or
either fix it to "0" if you want to treat al ofl them

-p

  This element represents the seed pattern to be searched

  * examples of seed patterns:
            - PatternHunter  : ###__##_#__###
            - Mandala        : ###__#_##_###   (forcing small span)
                               ####_##_###
            - YASS           : #@##_#__##__#@# (on Bernoulli
            model with constrains on seed jokers/tr-free elements)
                               ##@_#@#__#_###  (on pure Bernoulli model)
            model with mow (minimally overlapping words) seeds
                               RYNNNNNNnnnNNNNN

            -  2 seeds       :
               some examples to detect :
                    - very small random regions :
                      ###-###-####,###-#--#--#-####
                    -      small random regions :
                      ##-#----###-####,###--#-#-#--#--###
                    -            random regions :
                      ##-#-##---##-##--#,##-###--#---#----###
                    -      large random regions :
                      ##--#---#-#--###---##,##-#--#-#--#--##-##
                    - very small transition rich random regions :
                      ###@##-##-#@#,###-@-#--@--#####
                    -      small transition rich random regions :
                      ##@#-#-##@-###,#-##--#--#@#--@-###
                    -            transition rich random regions :
                      ###-#----#-#--#@#-@#,##-#--@#-#-###--@#
                    -      large transition rich random regions :
                      #@#--#----###--@-##,#-#-#@---#-#-@-##-##
               other examples :
                    mixed regions (chr-inver-fungi) :
                      #@-##-##-#--@-###,#-##@---##---#---#@#-#
                    mixed regions (chr-best)        :
                      #-###@#--#-#-@##,###@-#-#------@#-#--##
                    mixed regions (chr-avg)         :
                      ##-#-#@#-#--@###,#-##@--#----#--##@##

-e : alignment Entropy

  YASS does a filtering step based on the triplet composition
  of the alignment

      -e 0.0  : filter is off.
      -e 3.10 : filter is set to its default level
      -e 5.99 : filter is set to its highest level (don't use this)

  PS : this option is subject to changes in future versions

-r : reverse strain considered

  YASS considers both forward and complementary reverse strain
  of the first sequence if -r 2 set. You can select with -r 0 only
  direct repeats or only complementary inverted ones with -r 1

  (default is both forward and complementary : -r 2 )

-S Select query sequence from a multifasta file (default 1)

 If the first file provided is not fasta but multifasta, you can choose
 (using this parameter) which fasta sequence will be the query (by
 default the first one).

-T “anti Tandem trick”

 Forbid aligning too close regions (e.g. Tandem repeats)
 valid only for comparing a single-sequence file against itself

-a -i -m : seed grouping parameters

 YASS groups seeds before extension and then extends them once grouped.
 These parameters enable you to modify the grouping criteria and extention
 limits that are fixed (before post processing).

 "-m" gives the expected mutation rate (25%) : it can be increased to 30%
 or 40% but no more in practice.

 "-i" gives the expected indel rate (8%) : can be also modified to ~ 10%

 "-a" give the bound so 95% of (when fixed to 5%) of the distribution of
 indels/mutations between seeds are captured during the extention process.

-W <min,max> -w : Post-processing parameters

 In order to group some consecutive alignments into a better
 scoring one, post processing tries to group neighbor alignments in
 an iterative process : by applying several time a sliding windows
 on the text and estimating score of possible groups formed.
 Windows size can be controlled according to a geometric pattern
 <mul> and two bounds <min,max>.

 -w 0 (or 1) disables this post-processing step.

References

YASS is presented in the following paper. If you use YASS, please cite one (or more) of the following papers in your work :

[1] L. Noe, G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, 2005, Nucleic Acids Research, 33(2):W540-W543.

[2] L. Noe, G. Kucherov, Improved hit criteria for DNA local alignment, 2004, BMC Bioinformatics, 5:149.